Have you actually visually looked at the four wires on the problem coil. My thinking is that if flipper starts to become weak it is a wire getting ready to break away from the coil lug.

Thicker two are for the power winding. The small gauge is for the hold.

So look at the actual connection of coil to lugs, you may need to use x10 jewelers scope with good light to see.

I am not fully understanding your flip idea. But I would say NO. Coils are wired according to which lugs the coil wires go to and then depending on the diode . If you reverse leads you may be forward biasing the diode which would act as a short, and just blow the fuse.

Diode test power off.
one leg of diode has to be lifted. Red lead on unbanded side and Black on banded should give you reading of .5-.7 reverse leads and you should get no reading.

Very good call on the diode shorted.

Sounds like your EOS and switch to energize the upper flipper may be reversed.
Compare with other side if you can.